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- PDB-5fbv: PI4KB in complex with Rab11 and the MI364 Inhibitor -

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Basic information

Entry
Database: PDB / ID: 5fbv
TitlePI4KB in complex with Rab11 and the MI364 Inhibitor
Components
  • Phosphatidylinositol 4-kinase beta,Phosphatidylinositol 4-kinase beta
  • Ras-related protein Rab-11A
KeywordsTRANSFERASE / Inhibitor / Complex / Kinase / Lipid
Function / homology
Function and homology information


: / regulation of protein localization to centrosome / synaptic vesicle endosomal processing / : / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / regulation of endocytic recycling / establishment of protein localization to organelle / postsynaptic recycling endosome / positive regulation of mitotic cytokinetic process ...: / regulation of protein localization to centrosome / synaptic vesicle endosomal processing / : / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / regulation of endocytic recycling / establishment of protein localization to organelle / postsynaptic recycling endosome / positive regulation of mitotic cytokinetic process / establishment of vesicle localization / rough endoplasmic reticulum membrane / regulation of cilium assembly / amyloid-beta clearance by transcytosis / regulation of protein transport / presynaptic endosome / neurotransmitter receptor transport, endosome to postsynaptic membrane / exosomal secretion / vesicle-mediated transport in synapse / plasma membrane to endosome transport / VxPx cargo-targeting to cilium / Synthesis of PIPs at the Golgi membrane / regulation of vesicle-mediated transport / protein transmembrane transport / myosin V binding / RAB geranylgeranylation / astral microtubule organization / multivesicular body assembly / phosphatidylinositol biosynthetic process / protein localization to cilium / melanosome transport / Golgi to plasma membrane protein transport / establishment of protein localization to membrane / TBC/RABGAPs / protein localization to cell surface / syntaxin binding / dynein light intermediate chain binding / mitotic metaphase chromosome alignment / lysosome organization / phosphatidylinositol phosphate biosynthetic process / phosphatidylinositol-mediated signaling / inner ear development / exocytosis / cleavage furrow / positive regulation of epithelial cell migration / mitotic spindle assembly / positive regulation of G2/M transition of mitotic cell cycle / transport vesicle / phagocytic vesicle / vesicle-mediated transport / multivesicular body / 14-3-3 protein binding / Anchoring of the basal body to the plasma membrane / receptor-mediated endocytosis / cytoplasmic vesicle membrane / trans-Golgi network membrane / small monomeric GTPase / regulation of cytokinesis / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / centriole / trans-Golgi network / regulation of long-term neuronal synaptic plasticity / recycling endosome / Schaffer collateral - CA1 synapse / recycling endosome membrane / spindle pole / neuron projection development / endocytic vesicle membrane / Vasopressin regulates renal water homeostasis via Aquaporins / synaptic vesicle membrane / G protein activity / cytoplasmic vesicle / microtubule binding / vesicle / mitochondrial outer membrane / endosome / Golgi membrane / GTPase activity / centrosome / GTP binding / perinuclear region of cytoplasm / glutamatergic synapse / Golgi apparatus / signal transduction / protein-containing complex / extracellular exosome / ATP binding / membrane / cytoplasm / cytosol
Similarity search - Function
: / : / PI4KB/PIK1, accessory (PIK) domain / : / Small GTPase Rab domain profile. / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site ...: / : / PI4KB/PIK1, accessory (PIK) domain / : / Small GTPase Rab domain profile. / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Protein kinase-like domain superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-5W3 / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / Ras-related protein Rab-11A / Phosphatidylinositol 4-kinase beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.285 Å
AuthorsChalupska, D. / Mejdrova, I. / Nencka, R. / Boura, E.
CitationJournal: To Be Published
Title: PI4KB in complex with Rab11 and the MI364 Inhibitor
Authors: Chalupska, D. / Mejdrova, I. / Nencka, R. / Boura, E.
History
DepositionDec 14, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphatidylinositol 4-kinase beta,Phosphatidylinositol 4-kinase beta
B: Ras-related protein Rab-11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,1144
Polymers90,0782
Non-polymers1,0362
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-16 kcal/mol
Surface area28870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.536, 102.782, 186.141
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phosphatidylinositol 4-kinase beta,Phosphatidylinositol 4-kinase beta / PtdIns 4-kinase beta / NPIK / PI4K92 / PI4KB


Mass: 65264.766 Da / Num. of mol.: 1 / Fragment: UNP Residues 128-422, 523-799
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PI4KB, PIK4CB / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UBF8, 1-phosphatidylinositol 4-kinase
#2: Protein Ras-related protein Rab-11A / Rab-11 / YL8


Mass: 24813.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB11A, RAB11 / Production host: Escherichia coli (E. coli) / References: UniProt: P62491
#3: Chemical ChemComp-5W3 / ~{N}-[2-[[6-chloranyl-3-[3-(2-hydroxyethylsulfamoyl)-4-methoxy-phenyl]-2-methyl-imidazo[1,2-b]pyridazin-8-yl]amino]ethy l]ethanamide / MI364


Mass: 496.968 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H25ClN6O5S
#4: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3S

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.15M amonium sulfate, 0.1M MEW pH=6, 15% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 3.28→46.97 Å / Num. obs: 14745 / % possible obs: 99.01 % / Redundancy: 3.44 % / Rmerge(I) obs: 0.23 / Net I/σ(I): 7.63 / Num. measured all: 50723
Reflection shellResolution: 3.28→3.4 Å / Mean I/σ(I) obs: 0.95

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D0L

4d0l


Resolution: 3.285→46.966 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2814 734 5 %Random selection
Rwork0.2371 ---
obs0.2394 14675 98.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.285→46.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5012 0 65 0 5077
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125176
X-RAY DIFFRACTIONf_angle_d1.5437010
X-RAY DIFFRACTIONf_dihedral_angle_d15.1751890
X-RAY DIFFRACTIONf_chiral_restr0.072796
X-RAY DIFFRACTIONf_plane_restr0.011878
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2854-3.5390.44711400.38062680X-RAY DIFFRACTION97
3.539-3.89490.33021420.29572716X-RAY DIFFRACTION98
3.8949-4.45820.30811480.2292784X-RAY DIFFRACTION99
4.4582-5.61540.27871480.22522802X-RAY DIFFRACTION100
5.6154-46.97040.22331560.19872959X-RAY DIFFRACTION99

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